751: Molecular basis of TRPM3 – an ion channel involved in pain and brain disease

Topic: Experimental (Non-clinical) Human Studies
Subtopic: Non -specific to any diagnosis, Drug development, Pain mechanisms (e.g. descending inhibitory control, placebo, inflammation)

Background and Aims: Transient Receptor Potential melastatin 3 (TRPM3) is a temperature-sensitive ionotropic neurosteroid receptor within the TRP superfamily of cation channels. In the peripheral nervous system, TRPM3 is expressed and contributes to the detection of noxious heat. Under pathological conditions such as inflammation or neuropathy, TRPM3 channel activity is increased, contributing to sensory hypersensitivity and ongoing pain. In addition, TRPM3 is expressed in various neuronal and non-neuronal cells in the developing and adult brain, but its role in brain function is not well established. Notably, gain-of-function mutations in TRPM3 cause a spectrum of neurodevelopmental disorders, characterized by a variety of neurological symptoms, including developmental delay, hypotonia, seizures and often alterations in heat- or pain sensitivity. Therefore, strategies to modify TRPM3 activity represent important new therapeutic avenues to treat pathological pain and brain disorders. Despite the therapeutic promise of TRPM3 antagonists, the molecular mechanisms by which ligands modulate channel gating remain poorly understood.

Methods: cryo-electron microscopy (cryo-EM)
Functional studies, such as electrophysiology recording (patch-clamp), calcium imaging assay

Results: we characterize a common promiscuous ligand-binding pocket between transmembrane helices S1–S4, where several chemically distinct natural and synthetic agonists and antagonist interact with TRPM3. Despite the promiscuity of the ligand-binding pocket, Our data reveal its striking an unexpected stereoselectivity for the non-natural flavonoid enantiomer of the antagonist isosakuranetin and the (R)-enantiomer of the the agonist CIM0216. Mutations within the ligand-binding pocket—including new variants identified in patients—alter ligand affinity and, in some cases, invert the functional outcome of ligand binding. These findings underpin the stereoselectivity and functional plasticity of the ligand-binding pocket, where subtle changes in the interaction between TRPM3 and small-molecule ligands can have strongly divergent effects on channel gating, with important ramifications for TRPM3-targeted drug development.

Conclusions: An overall conclusion of our study is that the ligand binding pocket in the VSLD of TRPM3 exhibits a high degree of ligand promiscuity. Indeed, the same cavity forms the interaction side for both activating and inhibitory ligands, and apparently subtle changes to ligand and binding pocket can change the directionality of the effect of ligand binding on channel gating.
Mutations at these residues not only influence binding of the ligands to their binding site, but also affect the conformational changes that couple ligand binding in the VSLD to channel gating. The promiscuity and stereoselectivity of the ligand binding site adds a layer of complexity to structure-aided design approaches to develop novel pharmacological tools targeting TRPM3.

References: 1 Wagner, T. F. et al. Transient receptor potential M3 channels are ionotropic steroid receptors in pancreatic beta cells. Nat Cell Biol 10, 1421-1430 (2008). https://doi.org:10.1038/ncb1801
2 Vriens, J. et al. TRPM3 is a nociceptor channel involved in the detection of noxious heat. Neuron 70, 482-494 (2011). https://doi.org:10.1016/j.neuron.2011.02.051
3 Alkhatib, O. et al. Promiscuous G-Protein-Coupled Receptor Inhibition of Transient Receptor Potential Melastatin 3 Ion Channels by Gbetagamma Subunits. J Neurosci 39, 7840-7852 (2019). https://doi.org:10.1523/JNEUROSCI.0882-19.2019
4 Su, S., Yudin, Y., Kim, N., Tao, Y. X. & Rohacs, T. TRPM3 Channels Play Roles in Heat Hypersensitivity and Spontaneous Pain after Nerve Injury. J Neurosci 41, 2457-2474 (2021). https://doi.org:10.1523/JNEUROSCI.1551-20.2020
5 Vandewauw, I. et al. A TRP channel trio mediates acute noxious heat sensing. Nature 555, 662-666 (2018). https://doi.org:10.1038/nature26137
6 Aloi, V. D. et al. TRPM3 as a novel target to alleviate acute oxaliplatin-induced peripheral neuropathic pain. Pain 164, 2060-2069 (2023). https://doi.org:10.1097/j.pain.0000000000002906
7 Mulier, M. et al. Upregulation of TRPM3 in nociceptors innervating inflamed tissue. Elife 9 (2020). https://doi.org:10.7554/eLife.61103
8 Vanneste, M. et al. TRPM3 Is Expressed in Afferent Bladder Neurons and Is Upregulated during Bladder Inflammation. Int J Mol Sci 23 (2021). https://doi.org:10.3390/ijms23010107
9 Zhao, M. et al. Upregulation of transient receptor potential cation channel subfamily M member-3 in bladder afferents is involved in chronic pain in cyclophosphamide-induced cystitis. Pain 163, 2200-2212 (2022). https://doi.org:10.1097/j.pain.0000000000002616
10 King, J. W. et al. Expression and function of transient receptor potential melastatin 3 in the spinal afferent innervation of the mouse colon. Am J Physiol Gastrointest Liver Physiol 326, G176-G186 (2024). https://doi.org:10.1152/ajpgi.00230.2023
11 Burglen, L. et al. Gain-of-function variants in the ion channel gene TRPM3 underlie a spectrum of neurodevelopmental disorders. Elife 12 (2023). https://doi.org:10.7554/eLife.81032
12 Held, K. & Toth, B. I. TRPM3 in Brain (Patho)Physiology. Front Cell Dev Biol 9, 635659 (2021). https://doi.org:10.3389/fcell.2021.635659
13 Dyment, D. A. et al. De novo substitutions of TRPM3 cause intellectual disability and epilepsy. Eur J Hum Genet 27, 1611-1618 (2019). https://doi.org:10.1038/s41431-019-0462-x
14 Van Hoeymissen, E. et al. Gain of channel function and modified gating properties in TRPM3 mutants causing intellectual disability and epilepsy. Elife 9 (2020). https://doi.org:10.7554/eLife.57190
15 Zhao, S., Yudin, Y. & Rohacs, T. Disease-associated mutations in the human TRPM3 render the channel overactive via two distinct mechanisms. Elife 9 (2020). https://doi.org:10.7554/eLife.55634
16 Lines, M. A. et al. Phenotypic spectrum of the recurrent TRPM3 p.(Val837Met) substitution in seven individuals with global developmental delay and hypotonia. Am J Med Genet A 188, 1667-1675 (2022). https://doi.org:10.1002/ajmg.a.62673
17 Dyment, D., Lines, M. & Innes, A. M. in GeneReviews((R)) (eds M. P. Adam et al.) (2023).
18 Roelens, R., Peigneur, A. N. F., Voets, T. & Vriens, J. Neurodevelopmental disorders caused by variants in TRPM3. Biochim Biophys Acta Mol Cell Res 1871, 119709 (2024). https://doi.org:10.1016/j.bbamcr.2024.119709
19 Jolitz, L. et al. Phenotype Spectrum of TRPM3-Associated Disorders. Ann Neurol 97, 561-570 (2025). https://doi.org:10.1002/ana.27141
20 Straub, I. et al. Flavanones that selectively inhibit TRPM3 attenuate thermal nociception in vivo. Mol Pharmacol 84, 736-750 (2013). https://doi.org:10.1124/mol.113.086843

Presenting Author: Bahar Bazeli
Submitting Author: Bahar Bazeli

Senior Author: Thomas Voets

IASP 2026 Global Year theme of Neuropathic Pain: Yes

• Alexander V Shkumatov - VIB-VUB Center for Structural Biology
• Stephan Schenck - VIB-VUB Center for Structural Biology
• Janine D Brunner - VIB-VUB Center for Structural Biology
• Thomas Voets - VIB-KU Leuven Center for Brain & Disease Research